The Cipher
by Marc Vun Kannon
Summary: He had his orders. He did his duty. My take on the assassination that wasn't, in First Date.
1. Chapter 1

**A/N** The termination order on Chuck in the beginning of Season 2 was a typical example of a plot device created for dramatic effect that makes very little sense when examined up close. Both illegal and immoral, it really paints most of the characters in some very unpleasant colors, and unsurprisingly was used and dropped with as much speed as they could.

Lots of fanfic authors deal with this dilemma in a variety of ways, usually unsatisfying, at least to me. (I did two myself and I'm not entirely happy about either of them.) The most recent example, from **Becoming** , by Arya's Prayers, along with the stunningly good **Chuck vs Pillow Talk** , by AgentInWaiting, gave me the idea for this story. It's short, just my attempt to make sense of it all. The goal here was to present an interpretation of events that stayed canon, but allows our heroes to be heroes.

* * *

He used the Morgan Door, of course.

Chuck's room was dark, so he flashed a low-beam light to get his bearings, and spot potential booby-traps. He expected none, but the day he acted on his expectations instead of solid intel was the day he retired, probably feet first. As expected, he saw none, Bartowskis being clean freaks and all, and so he dropped the beam.

The light coming under the door was enough to get him there, and he paused, listening. He didn't want to be here, but he had his orders. Failure to comply would only get them all killed, and not as nicely. If it had to be done, he wanted it to be done nicely. Clean, quick, and painless. Save the nasty stuff for those who deserved it. Chuck should never see him coming.

He heard a voice. Who was Chuck talking to? This whole operation had been planned down to the last detail. He had some margin in it, but not for the usual stupid screwups that plagued most of their other operations, no matter how successfully they'd turned out. He raised his silenced pistol, and cracked open the door.

No one in view. He could hear Chuck talking, but he didn't seem to be talking to anyone. What was he doing, rehearsing? He rolled his eyes. Overthinking everything about his dinner with Walker, as usual. Life would be so much easier if one of these clueless idiots would just _say_ something. Too bad tonight had to be the end of all their chances.

The phone in his pocket vibrated silently. Time for the next phase. With a dental mirror he checked the living room. Chuck stood by the table, forgetting to keep his back to the wall, again. Just as well, this time.

Someone knocked on the door, and he shrank back into the shadows, checking his watch. If that was Walker, she was a little early. She was supposed to find the body, that was the plan. Killing the kid in front of her was an avoidable cruelty, but as details went it was pretty negotiable. He tracked his target across the floor by sound, waiting for a clear shot. He'd only have a second before the door opened and spoiled everything.

His finger was squeezing the trigger when Sarah launched herself through the door, displacing his target and talking a mile a minute, not letting Chuck get a word in edgewise. A minor miracle. He listened as she talked, backing away from the scene of the almost-murder.

So the Cipher blew up, no surprise there. No new Intersect, so they still needed Bartowski. Time to go. They'd be going over to his home base soon, he had to look innocent.

* * *

As he crossed the courtyard he picked up his motion detector, aimed at the tunnel and linked to his phone, so he'd know when Walker arrived. In the apartment, he racked his gun and washed his hands, going to his surveillance gear. The lovebirds were still talking, no surprise there either, although for the life of him he didn't know why they should be so surprised.

The Cipher was easy enough to booby-trap, after all, just in case those Fulcrum traitors managed to get a hold of it again. Which, amazingly, they had. And they could be expected to gimmick it too, something crude, of course. So easily found, the guys looking for the gimmicks stopped looking, just a bit too soon.

It wouldn't have been a problem if someone hadn't been in a rush. Someone wanted Chuck dead pretty damn bad, after all, some traitorous, treacherous bastard, after all the moron had done for his country. Whoever it was would almost certainly pounce on the Cipher and use it, before it could get stolen again. Fifty-fifty who would get it, Beckman or Graham, but for the sake of his agency he hoped it was Graham, and it seems he was right. _Never trusted that guy._ Hopefully, with him gone Beckman would straighten out and fly right.

He smiled, and rewound the whole event, watching as his every step was captured, proof that he was on the job, ready to do his duty, until interrupted by an act of God.

Or an act of Casey.


	2. Chapter 2

**A/N** I was only planning the one story about this topic, but as reviewer James Mowery pointed out, there had been a couple of conversations between Beckman and Casey on the subject of the termination order. She had some responsibility for it that had to be addressed, otherwise she still looks like a bit of a schmuck.

* * *

"He flew a helicopter." Beckman flipped pages in Casey's report, looking for the footnotes, where the action really was. Words like 'video' and 'game' leapt out at her, even more terrifying in combination, and she was never reluctant to speak her mind to junior officers. Of course, it helped to have juniors who knew her mind already. "Do we really have the situation in hand or should Mr. Bartowski be in our care full time?"

Casey's voice came back in a soft growl, his version of being quiet. "You know how I feel, General–" As much as anyone did. Her attack dog found _having_ feelings distasteful, much less talking about them. "–but for now we're in control."

 _Good dog._ She threw him a treat. "Then Chuck stays where he is. But, uh, don't get too comfortable, Major Casey. The new Intersect will be up and running in six months." Hopefully they could keep Bartowski alive that long.

Casey sounded only mildly curious. "And what happens to Chuck when this is done?"

She sounded only mildly interested. "Well…you'll do what you do best."

* * *

Six months later, after yet another mission nearly blown by Bartowski emotionalism and then saved by Bartowski cleverness and great good luck…

"Major, I'm calling to inform you that the beta version of the Intersect computer was successful." She heard party music in the background, so she spoke a bit louder. "This means that the new Intersect should be up and running soon. Once the new computer is online, it will be time to take care of Bartowski."

A brief pause before her subordinate replied. "Roger that."

"I…hope that you have not grown too fond of the subject." After having read his report, she doubted that, being aware as most people who knew him were how much he loved his car. "I would hate for you to be…compromised." Except for the way she wanted him to be compromised.

"I understand my orders, General."

Of course he did. "Oh, and John?"

"Yeah?"

"Happy Holidays."

* * *

Soon wasn't soon enough. That beta version had been rebuilt and redesigned, as new exploits from her best team gave the designers new ideas in their continuing efforts to reverse engineer Bartowski's brain. When the stories came out about how Bartowski had gotten himself and his NSA handler thrown into a pool from a hotel balcony, she had all further reports remanded into the care of the only man who took security more seriously than her, the designer of the security features for the Federal vaults. No one spoke to him.

Their fun interrupted, the boffins retaliated by getting all huffy about security, and the process began again. This time it was imperative to protect the data, so that it would never be stolen as it had the first time. A chance remark from her aid in the lunchroom, about a home remodeling project of all things, inspired them to redesign the entire encryption process. Rather than store the data encrypted, ready to be stolen, it was encrypted and merged with the images as the final step in the process by a piece of hardware they called the Cipher.

Which got stolen. And recovered. And stolen again. And recovered again. When the piece and the reports arrived almost simultaneously, Beckman pounced on the reports as Graham sent the Cipher off to analysis, to check for the usual Fulcrum tricks.

She was busy redacting all of the revealing bits from Bartowski's report, so she could send it to her pet boffins for a translation into English, when the news came in. Graham had jumped the gun, tried to use the new Intersect without the NSA being there, and had gotten blown up for his trouble. Security recordings survived, even if the cameras that took them didn't, and the mocking words from Fulcrum were clearly visible, right before the end.

Immediately she had her aide send Major Casey a priority message, cancelling all orders for tonight, afraid that she was too late. And she had been. Her monitor chimed with John's incoming call even as Mr. Clark left the room. She listened to his verbal report (there would be no written one, not for something like this) and watched the recordings. He was obeying his orders, only to be stopped at the last minute by the sudden appearance of Agent Walker, with her news of Graham's tragic death. Beckman commended John for his initiative in aborting the mission, ended the call, and went to bed.

It was so nice to have subordinates who knew their commander's mind, and did what she wanted rather than what she ordered.

The easiest way to prevent an illegal order from being carried out was to issue it herself, to the right person. John Casey might have been willing to burn his asset, if his General had so ordered, but the fact that she _didn't_ order it told him what his orders really were, and after the hotel incident he wouldn't have done it, even if she had ordered. Manipulating the boffins in the lab to continually redesign was an amusing pastime, but never her true goal. They only had to drop four hints in the head guy's vicinity, rather than the usual six or seven, before he had his sudden inspiration. Thus the Cipher was born, and so easy to steal, too. Thank God John and his team were there to recover it.

As she lay there in the dark she considered that last message, 'Fulcrum thanks you,' and how she would respond to this latest act of sabotage. Now was not the time to experiment with untried technologies. Clearly Fulcrum was more of a threat than they'd thought. Whatever had destroyed the lab had to have been remarkably subtle to get past the boys in security. Fulcrum wasn't known to be that subtle, yet somehow they'd managed it.

Just like John.

* * *

 **A/N2** This chapter is a little less clear-cut than the first. Casey's goals were much clearer, whereas Beckman is fighting a number of political fires and needs a bit of deniability, as well as adaptability. Her situation with Graham is hinted at, but has already been described more baldly in chapter one. The outcome is consistent with her stated goal (later in season 2) of keeping the Intersect with Chuck. Casey's actions are her tool, but he is operating independently. She isn't controlling him, and the results aren't always what she wanted, or planned for. (This model comes from one of WvonB's stories.)

As I was reviewing the early episodes for the dialog of her calls with Casey, I realized that there were seven weeks between Crown Vic and Undercover Lover/Marlin. Somewhere in those seven weeks Chuck, Sarah, and Casey transformed into Team B. Beckman in this story recognizes that change, even if she doesn't know the cause. I toss that out there for those who like to write more original Chuck stories than I do. Hopefully someone will tell the story of those seven weeks.


End file.
